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If you mean that you ran etc-update then it probably replaced your webmin config with an updated one (overwriting any modifications you had made to the config) you will have to re edit the webmin config to have it work again then add /etc/conf.d/webmin to CONFIG_PROTECT="" in /etc/make.conf (i think the file is /etc/conf.d/webmin but I dont use it so you will have to double check that for your self).

On a side note...dispatch-conf is much better than etc-update. You just need to emerge rcs && mkdir /etc/config-archive. It has the same functionality, but it uses rcs to keep a backup of all the configs you replace (in revision-style).

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